Has anyone tried using the 16" Rally wheels with the LS1 brake conversion? I am running both the front and rear disc on my 68 and trying to decide on wheels. I really wanted to keep the stock look if at all possible. Any help would be greatly appreciated.

I bought a 16" ralley wheel from Summit to try, and it wouldn't fit over the 12" LS1 brakes on my car, so I sent it back for credit. Like you I wanted the stock look and had falsely assumed a 15" wheel would fit over a 12" rotor and caliper.
It seems they use the same center section as the 15" wheel, but just weld a larger rim around it. Another option you could consider would be a 16" billet aluminum wheel from Wheel Vintiques, I believe they would fit, but they are expensive. http://www.wheelvintiques.com/
I ended up selecting 16" Torque Thrust II wheel. 7" x 4" B/S front and 8" x 4.75" B/S rear. They clear the front calipers by about 1/4" in the radius and look like they were factory fit. They also look good on the car, click on the link in my signature to see photos.
From home I could send you a photo of two, if you like.